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Tecik M, Adan A. Emerging DNA Methylome Targets in FLT3-ITD-Positive Acute Myeloid Leukemia: Combination Therapy with Clinically Approved FLT3 Inhibitors. Curr Treat Options Oncol 2024; 25:719-751. [PMID: 38696033 PMCID: PMC11222205 DOI: 10.1007/s11864-024-01202-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2024] [Indexed: 07/04/2024]
Abstract
OPINION STATEMENT The internal tandem duplication (ITD) mutation of the FMS-like receptor tyrosine kinase 3 (FLT3-ITD) is the most common mutation observed in approximately 30% of acute myeloid leukemia (AML) patients. It represents poor prognosis due to continuous activation of downstream growth-promoting signaling pathways such as STAT5 and PI3K/AKT. Hence, FLT3 is considered an attractive druggable target; selective small FLT3 inhibitors (FLT3Is), such as midostaurin and quizartinib, have been clinically approved. However, patients possess generally poor remission rates and acquired resistance when FLT3I used alone. Various factors in patients could cause these adverse effects including altered epigenetic regulation, causing mainly abnormal gene expression patterns. Epigenetic modifications are required for hematopoietic stem cell (HSC) self-renewal and differentiation; however, critical driver mutations have been identified in genes controlling DNA methylation (such as DNMT3A, TET2, IDH1/2). These regulators cause leukemia pathogenesis and affect disease diagnosis and prognosis when they co-occur with FLT3-ITD mutation. Therefore, understanding the role of different epigenetic alterations in FLT3-ITD AML pathogenesis and how they modulate FLT3I's activity is important to rationalize combinational treatment approaches including FLT3Is and modulators of methylation regulators or pathways. Data from ongoing pre-clinical and clinical studies will further precisely define the potential use of epigenetic therapy together with FLT3Is especially after characterized patients' mutational status in terms of FLT3 and DNA methlome regulators.
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Affiliation(s)
- Melisa Tecik
- Bioengineering Program, Graduate School of Engineering and Science, Abdullah Gul University, Kayseri, Turkey
| | - Aysun Adan
- Department of Molecular Biology and Genetics, Faculty of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey.
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2
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Nayarisseri A, Bandaru S, Khan A, Sharma K, Bhrdwaj A, Kaur M, Ghosh D, Chopra I, Panicker A, Kumar A, Saravanan P, Belapurkar P, Mendonça Junior FJB, Singh SK. Epigenetic dysregulation in cancers by isocitrate dehydrogenase 2 (IDH2). ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:223-253. [PMID: 38960475 DOI: 10.1016/bs.apcsb.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Recent advances in genome-wide studies have revealed numerous epigenetic regulations brought about by genes involved in cellular metabolism. Isocitrate dehydrogenase (IDH), an essential enzyme, that converts isocitrate into -ketoglutarate (KG) predominantly in the tricarboxylic acid (TCA) cycle, has gained particular importance due to its cardinal role in the metabolic pathway in cells. IDH1, IDH2, and IDH3 are the three isomeric IDH enzymes that have been shown to regulate cellular metabolism. Of particular importance, IDH2 genes are associated with several cancers, including gliomas, oligodendroglioma, and astrocytomas. These mutations lead to the production of oncometabolite D-2-hydroxyglutarate (D-2-HG), which accumulates in cells promoting tumor growth. The enhanced levels of D-2-HG competitively inhibit α-KG dependent enzymes, inhibiting cell TCA cycle, upregulating the cell growth and survival relevant HIF-1α pathway, promoting DNA hypermethylation related epigenetic activity, all of which synergistically contribute to carcinogenesis. The present review discusses epigenetic mechanisms inIDH2 regulation in cells and further its clinical implications.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India.
| | - Srinivas Bandaru
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Department of Biotechnology, Koneru Lakshmaiah Educational Foundation (KLEF), Green Fields, Vaddeswaram, Andhra Pradesh, India
| | - Arshiya Khan
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Manmeet Kaur
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Dipannita Ghosh
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Aravind Panicker
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Abhishek Kumar
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Department of Biosciences, Acropolis Institute, Indore, Madhya Pradesh, India
| | - Priyadevi Saravanan
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Pranoti Belapurkar
- Department of Biosciences, Acropolis Institute, Indore, Madhya Pradesh, India
| | | | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Kim N, Byun S, Um SJ. Additional Sex Combs-like Family Associated with Epigenetic Regulation. Int J Mol Sci 2024; 25:5119. [PMID: 38791157 PMCID: PMC11121404 DOI: 10.3390/ijms25105119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The additional sex combs-like (ASXL) family, a mammalian homolog of the additional sex combs (Asx) of Drosophila, has been implicated in transcriptional regulation via chromatin modifications. Abnormal expression of ASXL family genes leads to myelodysplastic syndromes and various types of leukemia. De novo mutation of these genes also causes developmental disorders. Genes in this family and their neighbor genes are evolutionary conserved in humans and mice. This review provides a comprehensive summary of epigenetic regulations associated with ASXL family genes. Their expression is commonly regulated by DNA methylation at CpG islands preceding transcription starting sites. Their proteins primarily engage in histone tail modifications through interactions with chromatin regulators (PRC2, TrxG, PR-DUB, SRC1, HP1α, and BET proteins) and with transcription factors, including nuclear hormone receptors (RAR, PPAR, ER, and LXR). Histone modifications associated with these factors include histone H3K9 acetylation and methylation, H3K4 methylation, H3K27 methylation, and H2AK119 deubiquitination. Recently, non-coding RNAs have been identified following mutations in the ASXL1 or ASXL3 gene, along with circular ASXLs and microRNAs that regulate ASXL1 expression. The diverse epigenetic regulations linked to ASXL family genes collectively contribute to tumor suppression and developmental processes. Our understanding of ASXL-regulated epigenetics may provide insights into the development of therapeutic epigenetic drugs.
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Affiliation(s)
| | | | - Soo-Jong Um
- Department of Integrative Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Gwangjin-Gu, Seoul 05006, Republic of Korea; (N.K.)
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4
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Lee MK, Azizgolshani N, Zhang Z, Perreard L, Kolling FW, Nguyen LN, Zanazzi GJ, Salas LA, Christensen BC. Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors. Nat Commun 2024; 15:3635. [PMID: 38688903 PMCID: PMC11061294 DOI: 10.1038/s41467-024-47943-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Although intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify cell type-specific alterations to cytosine modifications in pediatric central nervous system tumors, we utilize a multi-omic approach that integrated bulk DNA cytosine modification data (methylation and hydroxymethylation) with both bulk and single-cell RNA-sequencing data. We demonstrate a large reduction in the scope of significantly differentially modified cytosines in tumors when accounting for tumor cell type composition. In the progenitor-like cell types of tumors, we identify a preponderance differential Cytosine-phosphate-Guanine site hydroxymethylation rather than methylation. Genes with differential hydroxymethylation, like histone deacetylase 4 and insulin-like growth factor 1 receptor, are associated with cell type-specific changes in gene expression in tumors. Our results highlight the importance of epigenomic alterations in the progenitor-like cell types and its role in cell type-specific transcriptional regulation in pediatric central nervous system tumors.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Surgery, Columbia University Medical Center, New York, NY, USA
| | - Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Laurent Perreard
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Fred W Kolling
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - George J Zanazzi
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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5
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Mecca M, Picerno S, Cortellino S. The Killer's Web: Interconnection between Inflammation, Epigenetics and Nutrition in Cancer. Int J Mol Sci 2024; 25:2750. [PMID: 38473997 DOI: 10.3390/ijms25052750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Inflammation is a key contributor to both the initiation and progression of tumors, and it can be triggered by genetic instability within tumors, as well as by lifestyle and dietary factors. The inflammatory response plays a critical role in the genetic and epigenetic reprogramming of tumor cells, as well as in the cells that comprise the tumor microenvironment. Cells in the microenvironment acquire a phenotype that promotes immune evasion, progression, and metastasis. We will review the mechanisms and pathways involved in the interaction between tumors, inflammation, and nutrition, the limitations of current therapies, and discuss potential future therapeutic approaches.
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Affiliation(s)
- Marisabel Mecca
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Simona Picerno
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Salvatore Cortellino
- Laboratory of Preclinical and Translational Research, Responsible Research Hospital, 86100 Campobasso, CB, Italy
- Scuola Superiore Meridionale (SSM), Clinical and Translational Oncology, 80138 Naples, NA, Italy
- S.H.R.O. Italia Foundation ETS, 10060 Candiolo, TO, Italy
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Uchiyama T, Kawai T, Nakabayashi K, Nakazawa Y, Goto F, Okamura K, Nishimura T, Kato K, Watanabe N, Miura A, Yasuda T, Ando Y, Minegishi T, Edasawa K, Shimura M, Akiba Y, Sato-Otsubo A, Mizukami T, Kato M, Akashi K, Nunoi H, Onodera M. Myelodysplasia after clonal hematopoiesis with APOBEC3-mediated CYBB inactivation in retroviral gene therapy for X-CGD. Mol Ther 2023; 31:3424-3440. [PMID: 37705244 PMCID: PMC10727956 DOI: 10.1016/j.ymthe.2023.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
Stem cell gene therapy using the MFGS-gp91phox retroviral vector was performed on a 27-year-old patient with X-linked chronic granulomatous disease (X-CGD) in 2014. The patient's refractory infections were resolved, whereas the oxidase-positive neutrophils disappeared within 6 months. Thirty-two months after gene therapy, the patient developed myelodysplastic syndrome (MDS), and vector integration into the MECOM locus was identified in blast cells. The vector integration into MECOM was detectable in most myeloid cells at 12 months after gene therapy. However, the patient exhibited normal hematopoiesis until the onset of MDS, suggesting that MECOM transactivation contributed to clonal hematopoiesis, and the blast transformation likely arose after the acquisition of additional genetic lesions. In whole-genome sequencing, the biallelic loss of the WT1 tumor suppressor gene, which occurred immediately before tumorigenesis, was identified as a potential candidate genetic alteration. The provirus CYBB cDNA in the blasts contained 108 G-to-A mutations exclusively in the coding strand, suggesting the occurrence of APOBEC3-mediated hypermutations during the transduction of CD34-positive cells. A hypermutation-mediated loss of oxidase activity may have facilitated the survival and proliferation of the clone with MECOM transactivation. Our data provide valuable insights into the complex mechanisms underlying the development of leukemia in X-CGD gene therapy.
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Affiliation(s)
- Toru Uchiyama
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan.
| | - Toshinao Kawai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Tokyo, Japan
| | - Yumiko Nakazawa
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Fumihiro Goto
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Center for Child Health and Development, Tokyo, Japan
| | - Toyoki Nishimura
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Koji Kato
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Nobuyuki Watanabe
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Akane Miura
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Toru Yasuda
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Yukiko Ando
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoko Minegishi
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Kaori Edasawa
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Marika Shimura
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Yumi Akiba
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Pediatric Hematology and Oncology, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoyuki Mizukami
- Department of Pediatrics, NHO Kumamoto Medical Center, Kumamoto, Japan
| | - Motohiro Kato
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Pediatric Hematology and Oncology, National Center for Child Health and Development, Tokyo, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Hiroyuki Nunoi
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Masafumi Onodera
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
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7
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Chen F, Dowerg B, Cordes T. The yin and yang of itaconate metabolism and its impact on the tumor microenvironment. Curr Opin Biotechnol 2023; 84:102996. [PMID: 37806082 DOI: 10.1016/j.copbio.2023.102996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/24/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023]
Abstract
The tumor microenvironment (TME) consists of a network of metabolically interconnected tumor and immune cell types. Macrophages influence the metabolic composition within the TME, which directly impacts the metabolic state and drug response of tumors. The accumulation of oncometabolites, such as succinate, fumarate, and 2-hydroxyglutarate, represents metabolic vulnerabilities in cancer that can be targeted therapeutically. Immunometabolites are emerging as metabolic regulators of the TME impacting immune cell functions and cancer cell growth. Here, we discuss recent discoveries on the potential impact of itaconate on the TME. We highlight how itaconate influences metabolic pathways relevant to immune responses and cancer cell proliferation. We also consider the therapeutic implications of manipulating itaconate metabolism as an immunotherapeutic strategy to constrain tumor growth.
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Affiliation(s)
- Fangfang Chen
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany; Research Group Cellular Metabolism in Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Birte Dowerg
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Thekla Cordes
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany; Research Group Cellular Metabolism in Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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8
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Heyes E, Wilhelmson AS, Wenzel A, Manhart G, Eder T, Schuster MB, Rzepa E, Pundhir S, D'Altri T, Frank AK, Gentil C, Woessmann J, Schoof EM, Meggendorfer M, Schwaller J, Haferlach T, Grebien F, Porse BT. TET2 lesions enhance the aggressiveness of CEBPA-mutant acute myeloid leukemia by rebalancing GATA2 expression. Nat Commun 2023; 14:6185. [PMID: 37794021 PMCID: PMC10550934 DOI: 10.1038/s41467-023-41927-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 09/22/2023] [Indexed: 10/06/2023] Open
Abstract
The myeloid transcription factor CEBPA is recurrently biallelically mutated (i.e., double mutated; CEBPADM) in acute myeloid leukemia (AML) with a combination of hypermorphic N-terminal mutations (CEBPANT), promoting expression of the leukemia-associated p30 isoform, and amorphic C-terminal mutations. The most frequently co-mutated genes in CEBPADM AML are GATA2 and TET2, however the molecular mechanisms underlying this co-mutational spectrum are incomplete. By combining transcriptomic and epigenomic analyses of CEBPA-TET2 co-mutated patients with models thereof, we identify GATA2 as a conserved target of the CEBPA-TET2 mutational axis, providing a rationale for the mutational spectra in CEBPADM AML. Elevated CEBPA levels, driven by CEBPANT, mediate recruitment of TET2 to the Gata2 distal hematopoietic enhancer thereby increasing Gata2 expression. Concurrent loss of TET2 in CEBPADM AML induces a competitive advantage by increasing Gata2 promoter methylation, thereby rebalancing GATA2 levels. Of clinical relevance, demethylating treatment of Cebpa-Tet2 co-mutated AML restores Gata2 levels and prolongs disease latency.
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Affiliation(s)
- Elizabeth Heyes
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Anna S Wilhelmson
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Wenzel
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Manhart
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Thomas Eder
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Mikkel B Schuster
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Edwin Rzepa
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Sachin Pundhir
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Teresa D'Altri
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Katrine Frank
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Coline Gentil
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Woessmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Jürg Schwaller
- Department of Biomedicine, University Children's Hospital Basel, Basel, Switzerland
| | | | - Florian Grebien
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria.
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
| | - Bo T Porse
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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9
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Palau A, Segerberg F, Lidschreiber M, Lidschreiber K, Naughton AJ, Needhamsen M, Jung LA, Jagodic M, Cramer P, Lehmann S, Carlsten M, Lennartsson A. Perturbed epigenetic transcriptional regulation in AML with IDH mutations causes increased susceptibility to NK cells. Leukemia 2023; 37:1830-1841. [PMID: 37495775 PMCID: PMC10457197 DOI: 10.1038/s41375-023-01972-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/05/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
Isocitrate dehydrogenase (IDH) mutations are found in 20% of acute myeloid leukemia (AML) patients. However, only 30-40% of the patients respond to IDH inhibitors (IDHi). We aimed to identify a molecular vulnerability to tailor novel therapies for AML patients with IDH mutations. We characterized the transcriptional and epigenetic landscape with the IDH2i AG-221, using an IDH2 mutated AML cell line model and AML patient cohorts, and discovered a perturbed transcriptional regulatory network involving myeloid transcription factors that were partly restored after AG-221 treatment. In addition, hypermethylation of the HLA cluster caused a down-regulation of HLA class I genes, triggering an enhanced natural killer (NK) cell activation and an increased susceptibility to NK cell-mediated responses. Finally, analyses of DNA methylation data from IDHi-treated patients showed that non-responders still harbored hypermethylation in HLA class I genes. In conclusion, this study provides new insights suggesting that IDH mutated AML is particularly sensitive to NK cell-based personalized immunotherapy.
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Affiliation(s)
- Anna Palau
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Filip Segerberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Michael Lidschreiber
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Katja Lidschreiber
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Aonghus J Naughton
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Lisa Anna Jung
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Patrick Cramer
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sören Lehmann
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
- Hematology Centre, Karolinska University Hospital, Stockholm, Sweden.
- Hematology Unit, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
| | - Mattias Carlsten
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
- Center for Cell Therapy and Allogeneic Stem Cell Transplantation, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden.
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
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10
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Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
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Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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11
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Rérolle D, de Thé H. The PML hub: An emerging actor of leukemia therapies. J Exp Med 2023; 220:e20221213. [PMID: 37382966 PMCID: PMC10309189 DOI: 10.1084/jem.20221213] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/29/2023] [Accepted: 06/09/2023] [Indexed: 06/30/2023] Open
Abstract
PML assembles into nuclear domains that have attracted considerable attention from cell and cancer biologists. Upon stress, PML nuclear bodies modulate sumoylation and other post-translational modifications, providing an integrated molecular framework for the multiple roles of PML in apoptosis, senescence, or metabolism. PML is both a sensor and an effector of oxidative stress. Emerging data has demonstrated its key role in promoting therapy response in several hematological malignancies. While these membrane-less nuclear hubs can enforce efficient cancer cell clearance, their downstream pathways deserve better characterization. PML NBs are druggable and their known modulators may have broader clinical utilities than initially thought.
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Affiliation(s)
- Domitille Rérolle
- Center for Interdisciplinary Research in Biology, Collège de France, Inserm, PSL Research University, Paris, France
- Université Paris Cité, Inserm U944, CNRS, GenCellDis, Institut de Recherche Saint-Louis, Paris, France
| | - Hugues de Thé
- Center for Interdisciplinary Research in Biology, Collège de France, Inserm, PSL Research University, Paris, France
- Université Paris Cité, Inserm U944, CNRS, GenCellDis, Institut de Recherche Saint-Louis, Paris, France
- Chaire d'Oncologie Cellulaire et Moléculaire, Collège de France, Paris, France
- Service d'Hématologie Biologique, Assistance Publique-Hôpitaux de Paris, Hôpital St. Louis, Paris, France
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12
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Niktoreh N, Weber L, Walter C, Karimifard M, Hoffmeister LM, Breiter H, Thivakaran A, Soldierer M, Drexler HG, Schaal H, Sendker S, Reinhardt D, Schneider M, Hanenberg H. Understanding WT1 Alterations and Expression Profiles in Hematological Malignancies. Cancers (Basel) 2023; 15:3491. [PMID: 37444601 DOI: 10.3390/cancers15133491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
WT1 is a true chameleon, both acting as an oncogene and tumor suppressor. As its exact role in leukemogenesis is still ambiguous, research with model systems representing natural conditions surrounding the genetic alterations in WT1 is necessary. In a cohort of 59 leukemia/lymphoma cell lines, we showed aberrant expression for WT1 mRNA, which does not always translate into protein levels. We also analyzed the expression pattern of the four major WT1 protein isoforms in the cell lines and primary AML blasts with/without WT1 mutations and demonstrated that the presence of mutations does not influence these patterns. By introduction of key intronic and exonic sequences of WT1 into a lentiviral expression vector, we developed a unique tool that can stably overexpress the four WT1 isoforms at their naturally occurring tissue-dependent ratio. To develop better cellular model systems for WT1, we sequenced large parts of its gene locus and also other important myeloid risk factor genes and revealed previously unknown alterations. Functionally, inhibition of the nonsense-mediated mRNA decay machinery revealed that under natural conditions, the mutated WT1 alleles go through a robust degradation. These results offer new insights and model systems regarding the characteristics of WT1 in leukemia and lymphoma.
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Affiliation(s)
- Naghmeh Niktoreh
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Lisa Weber
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Christiane Walter
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Mahshad Karimifard
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Lina Marie Hoffmeister
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Hannah Breiter
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Aniththa Thivakaran
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Maren Soldierer
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Hans Günther Drexler
- Faculty of Life Sciences, Technical University of Braunschweig, 38106 Braunschweig, Germany
| | - Heiner Schaal
- Institute of Virology, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Stephanie Sendker
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Markus Schneider
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Helmut Hanenberg
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany
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13
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Gunn K, Myllykoski M, Cao JZ, Ahmed M, Huang B, Rouaisnel B, Diplas BH, Levitt MM, Looper R, Doench JG, Ligon KL, Kornblum HI, McBrayer SK, Yan H, Duy C, Godley LA, Koivunen P, Losman JA. (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers. Cancer Discov 2023; 13:1478-1497. [PMID: 36847506 PMCID: PMC10238656 DOI: 10.1158/2159-8290.cd-22-0825] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/21/2022] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Oncogenic mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 occur in a wide range of cancers, including acute myeloid leukemia (AML) and glioma. Mutant IDH enzymes convert 2-oxoglutarate (2OG) to (R)-2-hydroxyglutarate [(R)-2HG], an oncometabolite that is hypothesized to promote cellular transformation by dysregulating 2OG-dependent enzymes. The only (R)-2HG target that has been convincingly shown to contribute to transformation by mutant IDH is the myeloid tumor suppressor TET2. However, there is ample evidence to suggest that (R)-2HG has other functionally relevant targets in IDH-mutant cancers. Here, we show that (R)-2HG inhibits KDM5 histone lysine demethylases and that this inhibition contributes to cellular transformation in IDH-mutant AML and IDH-mutant glioma. These studies provide the first evidence of a functional link between dysregulation of histone lysine methylation and transformation in IDH-mutant cancers. SIGNIFICANCE Mutant IDH is known to induce histone hypermethylation. However, it is not known if this hypermethylation is functionally significant or is a bystander effect of (R)-2HG accumulation in IDH-mutant cells. Here, we provide evidence that KDM5 inhibition by (R)-2HG contributes to mutant IDH-mediated transformation in AML and glioma. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Kathryn Gunn
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matti Myllykoski
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - John Z. Cao
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Manna Ahmed
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Bofu Huang
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Betty Rouaisnel
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bill H. Diplas
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael M. Levitt
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ryan Looper
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Keith L. Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Harley I. Kornblum
- Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
| | - Samuel K. McBrayer
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hai Yan
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cihangir Duy
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Lucy A. Godley
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - Julie-Aurore Losman
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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14
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Shao J, Shah S, Ganguly S, Zu Y, He C, Li Z. Classification of Acute Myeloid Leukemia by Cell-Free DNA 5-Hydroxymethylcytosine. Genes (Basel) 2023; 14:1180. [PMID: 37372359 PMCID: PMC10298116 DOI: 10.3390/genes14061180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Epigenetic abnormality is a hallmark of acute myeloid leukemia (AML), and aberrant 5-hydroxymethylcytosine (5hmC) levels are commonly observed in AML patients. As epigenetic subgroups of AML correlate with different clinical outcomes, we investigated whether plasma cell-free DNA (cfDNA) 5hmC could categorize AML patients into subtypes. We profiled the genome-wide landscape of 5hmC in plasma cfDNA from 54 AML patients. Using an unbiased clustering approach, we found that 5hmC levels in genomic regions with a histone mark H3K4me3 classified AML samples into three distinct clusters that were significantly associated with leukemia burden and survival. Cluster 3 showed the highest leukemia burden, the shortest overall survival of patients, and the lowest 5hmC levels in the TET2 promoter. 5hmC levels in the TET2 promoter could represent TET2 activity resulting from mutations in DNA demethylation genes and other factors. The novel genes and key signaling pathways associated with aberrant 5hmC patterns could add to our understanding of DNA hydroxymethylation and highlight the potential therapeutic targets in AML. Our results identify a novel 5hmC-based AML classification system and further underscore cfDNA 5hmC as a highly sensitive marker for AML.
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Affiliation(s)
- Jianming Shao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Shilpan Shah
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Siddhartha Ganguly
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Chuan He
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA
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15
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Del Moral-Morales A, Salgado-Albarrán M, Sánchez-Pérez Y, Wenke NK, Baumbach J, Soto-Reyes E. CTCF and Its Multi-Partner Network for Chromatin Regulation. Cells 2023; 12:1357. [PMID: 37408191 DOI: 10.3390/cells12101357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Architectural proteins are essential epigenetic regulators that play a critical role in organizing chromatin and controlling gene expression. CTCF (CCCTC-binding factor) is a key architectural protein responsible for maintaining the intricate 3D structure of chromatin. Because of its multivalent properties and plasticity to bind various sequences, CTCF is similar to a Swiss knife for genome organization. Despite the importance of this protein, its mechanisms of action are not fully elucidated. It has been hypothesized that its versatility is achieved through interaction with multiple partners, forming a complex network that regulates chromatin folding within the nucleus. In this review, we delve into CTCF's interactions with other molecules involved in epigenetic processes, particularly histone and DNA demethylases, as well as several long non-coding RNAs (lncRNAs) that are able to recruit CTCF. Our review highlights the importance of CTCF partners to shed light on chromatin regulation and pave the way for future exploration of the mechanisms that enable the finely-tuned role of CTCF as a master regulator of chromatin.
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Affiliation(s)
- Aylin Del Moral-Morales
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Marisol Salgado-Albarrán
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Yesennia Sánchez-Pérez
- Subdirección de Investigación, Instituto Nacional de Cancerología, Mexico City 14080, Mexico
| | - Nina Kerstin Wenke
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
- Computational BioMedicine Lab., University of Southern Denmark, DK-5230 Odense, Denmark
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
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16
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Duployez N, Vasseur L, Kim R, Largeaud L, Passet M, L'Haridon A, Lemaire P, Fenwarth L, Geffroy S, Helevaut N, Celli-Lebras K, Adès L, Lebon D, Berthon C, Marceau-Renaut A, Cheok M, Lambert J, Récher C, Raffoux E, Micol JB, Pigneux A, Gardin C, Delabesse E, Soulier J, Hunault M, Dombret H, Itzykson R, Clappier E, Preudhomme C. UBTF tandem duplications define a distinct subtype of adult de novo acute myeloid leukemia. Leukemia 2023:10.1038/s41375-023-01906-z. [PMID: 37085611 DOI: 10.1038/s41375-023-01906-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/06/2023] [Accepted: 04/17/2023] [Indexed: 04/23/2023]
Abstract
Tandem duplications (TDs) of the UBTF gene have been recently described as a recurrent alteration in pediatric acute myeloid leukemia (AML). Here, by screening 1946 newly diagnosed adult AML, we found that UBTF-TDs occur in about 3% of patients aged 18-60 years, in a mutually exclusive pattern with other known AML subtype-defining alterations. The characteristics of 59 adults with UBTF-TD AML included young age (median 37 years), low bone marrow (BM) blast infiltration (median 25%), and high rates of WT1 mutations (61%), FLT3-ITDs (51%) and trisomy 8 (29%). BM morphology frequently demonstrates dysmyelopoiesis albeit modulated by the co-occurrence of FLT3-ITD. UBTF-TD patients have lower complete remission (CR) rates (57% after 1 course and 76% after 2 courses of intensive chemotherapy [ICT]) than UBTF-wild-type patients. In patients enrolled in the ALFA-0702 study (n = 614 patients including 21 with UBTF-TD AML), the 3-year disease-free survival (DFS) and overall survival of UBTF-TD patients were 42.9% (95%CI: 23.4-78.5%) and 57.1% (95%CI: 39.5-82.8%) and did not significantly differ from those of ELN 2022 intermediate/adverse risk patients. Finally, the study of paired diagnosis and relapsed/refractory AML samples suggests that WT1-mutated clones are frequently selected under ICT. This study supports the recognition of UBTF-TD AML as a new AML entity in adults.
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Affiliation(s)
- Nicolas Duployez
- Université de Lille, Unité 1277-Canther, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France.
- Hematology Laboratory, Centre Hospitalier Universitaire (CHU) de Lille, Lille, France.
- Université Paris Cité, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, F-75010, Paris, France.
- Laboratoire de biologie médicale multisites SeqOIA - FMG2025, Paris, France.
| | - Loïc Vasseur
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - Rathana Kim
- Université Paris Cité, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
- Laboratoire de biologie médicale multisites SeqOIA - FMG2025, Paris, France
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Laëtitia Largeaud
- Hematology Laboratory, CHU Toulouse, INSERM 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Marie Passet
- Université Paris Cité, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
- Laboratoire de biologie médicale multisites SeqOIA - FMG2025, Paris, France
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Anaïs L'Haridon
- Laboratoire de biologie médicale multisites SeqOIA - FMG2025, Paris, France
| | - Pierre Lemaire
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Laurène Fenwarth
- Université de Lille, Unité 1277-Canther, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
- Hematology Laboratory, Centre Hospitalier Universitaire (CHU) de Lille, Lille, France
| | - Sandrine Geffroy
- Université de Lille, Unité 1277-Canther, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
- Hematology Laboratory, Centre Hospitalier Universitaire (CHU) de Lille, Lille, France
| | - Nathalie Helevaut
- Université de Lille, Unité 1277-Canther, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
- Hematology Laboratory, Centre Hospitalier Universitaire (CHU) de Lille, Lille, France
| | | | - Lionel Adès
- Université Paris Cité, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - Delphine Lebon
- Hematology Department, CHU Amiens-Picardie, Amiens, France
| | - Céline Berthon
- Hematology Department, Claude Huriez Hospital, CHU Lille, Lille, France
| | - Alice Marceau-Renaut
- Université de Lille, Unité 1277-Canther, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
- Hematology Laboratory, Centre Hospitalier Universitaire (CHU) de Lille, Lille, France
| | - Meyling Cheok
- Université de Lille, Unité 1277-Canther, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Juliette Lambert
- Hematology Department, Versailles Hospital, University Versailles-Saint-Quentin-en-Yvelines, Le Chesnay, France
| | - Christian Récher
- Service d'Hématologie, CHU Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Emmanuel Raffoux
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | | | - Arnaud Pigneux
- Hematology Department, CHU de Bordeaux, Bordeaux, France
| | - Claude Gardin
- Hematology Department, Avicenne Hospital, AP-HP, Bobigny, France
- Unité 3518, Saint-Louis Institute for Research, Université de Paris, Paris, France
| | - Eric Delabesse
- Hematology Laboratory, CHU Toulouse, INSERM 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Jean Soulier
- Université Paris Cité, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
- Laboratoire de biologie médicale multisites SeqOIA - FMG2025, Paris, France
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Mathilde Hunault
- Hematology Department, Université d'Angers, Université de Nantes, CHU Angers, Inserm, CNRS, CRCI2NA, SFR ICAT, F‑49000, Angers, France
- Fédération Hospitalo-Universitaire, Grand-Ouest Acute Leukemia, Angers, France
| | - Hervé Dombret
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
- Unité 3518, Saint-Louis Institute for Research, Université de Paris, Paris, France
| | - Raphael Itzykson
- Université Paris Cité, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - Emmanuelle Clappier
- Université Paris Cité, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
- Laboratoire de biologie médicale multisites SeqOIA - FMG2025, Paris, France
- Hematology Laboratory, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Claude Preudhomme
- Université de Lille, Unité 1277-Canther, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
- Hematology Laboratory, Centre Hospitalier Universitaire (CHU) de Lille, Lille, France
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17
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Cheng CK, Yung YL, Chan HY, Leung KT, Chan KYY, Leung AWK, Cheng FWT, Li CK, Wan TSK, Luo X, Pitts HA, Cheung JS, Chan NPH, Ng MHL. Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia. Commun Biol 2023; 6:356. [PMID: 37002311 PMCID: PMC10066286 DOI: 10.1038/s42003-023-04732-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Pediatric acute myeloid leukemia (AML) is an uncommon but aggressive hematological malignancy. The poor outcome is attributed to inadequate prognostic classification and limited treatment options. A thorough understanding on the genetic basis of pediatric AML is important for the development of effective approaches to improve outcomes. Here, by comprehensively profiling fusion genes as well as mutations and copy number changes of 141 myeloid-related genes in 147 pediatric AML patients with subsequent variant functional characterization, we unveil complex mutational patterns of biological relevance and disease mechanisms including MYC deregulation. Also, our findings highlight TP53 alterations as strong adverse prognostic markers in pediatric AML and suggest the core spindle checkpoint kinase BUB1B as a selective dependency in this aggressive subgroup. Collectively, our present study provides detailed genomic characterization revealing not only complexities and mechanistic insights into pediatric AML but also significant risk stratification and therapeutic strategies to tackle the disease.
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Affiliation(s)
- Chi-Keung Cheng
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuk-Lin Yung
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Hoi-Yun Chan
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Kam-Tong Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kathy Y Y Chan
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Alex W K Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Frankie W T Cheng
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi-Kong Li
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas S K Wan
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Luo
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Herbert-Augustus Pitts
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Joyce S Cheung
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Natalie P H Chan
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Margaret H L Ng
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China.
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18
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Mishra SK, Millman SE, Zhang L. Metabolism in acute myeloid leukemia: mechanistic insights and therapeutic targets. Blood 2023; 141:1119-1135. [PMID: 36548959 PMCID: PMC10375271 DOI: 10.1182/blood.2022018092] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Metabolic rewiring and cellular reprogramming are trademarks of neoplastic initiation and progression in acute myeloid leukemia (AML). Metabolic alteration in leukemic cells is often genotype specific, with associated changes in epigenetic and functional factors resulting in the downstream upregulation or facilitation of oncogenic pathways. Targeting abnormal or disease-sustaining metabolic activities in AML provides a wide range of therapeutic opportunities, ideally with enhanced therapeutic windows and robust clinical efficacy. This review highlights the dysregulation of amino acid, nucleotide, lipid, and carbohydrate metabolism in AML; explores the role of key vitamins and enzymes that regulate these processes; and provides an overview of metabolism-directed therapies currently in use or development.
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Affiliation(s)
| | - Scott E. Millman
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lingbo Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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19
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Ajuyah P, Mayoh C, Lau LMS, Barahona P, Wong M, Chambers H, Valdes-Mora F, Senapati A, Gifford AJ, D'Arcy C, Hansford JR, Manoharan N, Nicholls W, Williams MM, Wood PJ, Cowley MJ, Tyrrell V, Haber M, Ekert PG, Ziegler DS, Khuong-Quang DA. Histone H3-wild type diffuse midline gliomas with H3K27me3 loss are a distinct entity with exclusive EGFR or ACVR1 mutation and differential methylation of homeobox genes. Sci Rep 2023; 13:3775. [PMID: 36882456 PMCID: PMC9992705 DOI: 10.1038/s41598-023-30395-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
Diffuse midline gliomas (DMG) harbouring H3K27M mutation are paediatric tumours with a dismal outcome. Recently, a new subtype of midline gliomas has been described with similar features to DMG, including loss of H3K27 trimethylation, but lacking the canonical H3K27M mutation (H3-WT). Here, we report a cohort of five H3-WT tumours profiled by whole-genome sequencing, RNA sequencing and DNA methylation profiling and combine their analysis with previously published cases. We show that these tumours have recurrent and mutually exclusive mutations in either ACVR1 or EGFR and are characterised by high expression of EZHIP associated to its promoter hypomethylation. Affected patients share a similar poor prognosis as patients with H3K27M DMG. Global molecular analysis of H3-WT and H3K27M DMG reveal distinct transcriptome and methylome profiles including differential methylation of homeobox genes involved in development and cellular differentiation. Patients have distinct clinical features, with a trend demonstrating ACVR1 mutations occurring in H3-WT tumours at an older age. This in-depth exploration of H3-WT tumours further characterises this novel DMG, H3K27-altered sub-group, characterised by a specific immunohistochemistry profile with H3K27me3 loss, wild-type H3K27M and positive EZHIP. It also gives new insights into the possible mechanism and pathway regulation in these tumours, potentially opening new therapeutic avenues for these tumours which have no known effective treatment. This study has been retrospectively registered on clinicaltrial.gov on 8 November 2017 under the registration number NCT03336931 ( https://clinicaltrials.gov/ct2/show/NCT03336931 ).
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Affiliation(s)
- Pamela Ajuyah
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia
| | - Chelsea Mayoh
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Loretta M S Lau
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Paulette Barahona
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia
| | - Marie Wong
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Hazel Chambers
- Department of Anatomical Pathology, Royal Children's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Fatima Valdes-Mora
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Akanksha Senapati
- Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Andrew J Gifford
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,Anatomical Pathology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Colleen D'Arcy
- Department of Anatomical Pathology, Royal Children's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,Michael Rice Cancer Centre, Women's and Children's Hospital, Adelaide, SA, Australia.,South Australia Health and Medical Research Institute, Adelaide, SA, Australia.,South Australia Immunogenomics Cancer Institute, Adelaide, SA, Australia.,University of Adelaide, Adelaide, SA, Australia
| | - Neevika Manoharan
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Wayne Nicholls
- Oncology Service, Children's Health Queensland Hospital & Health Service, Brisbane, QLD, Australia
| | - Molly M Williams
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Paul J Wood
- Department of Paediatrics, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Mark J Cowley
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Vanessa Tyrrell
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Michelle Haber
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Paul G Ekert
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - David S Ziegler
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia. .,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia. .,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia. .,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia.
| | - Dong-Anh Khuong-Quang
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia. .,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
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20
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Lee MK, Azizgolshani N, Zhang Z, Perreard L, Kolling FW, Nguyen LN, Zanazzi GJ, Salas LA, Christensen BC. Hydroxymethylation alterations in progenitor-like cell types of pediatric central nervous system tumors are associated with cell type-specific transcriptional changes. RESEARCH SQUARE 2023:rs.3.rs-2517758. [PMID: 36909536 PMCID: PMC10002842 DOI: 10.21203/rs.3.rs-2517758/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Although intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify cell type-specific alterations to cytosine modifications in pediatric central nervous system tumors we utilized a multi-omic approach that integrated bulk DNA cytosine modification data (methylation and hydroxymethylation) with both bulk and single-cell RNA-sequencing data. We demonstrate a large reduction in the scope of significantly differentially modified cytosines in tumors when accounting for tumor cell type composition. In the progenitor-like cell types of tumors, we identified a preponderance differential CpG hydroxymethylation rather than methylation. Genes with differential hydroxymethylation, like HDAC4 and IGF1R, were associated with cell type-specific changes in gene expression in tumors. Our results highlight the importance of epigenomic alterations in the progenitor-like cell types and its role in cell type-specific transcriptional regulation in pediatric CNS tumors.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Cardiothoracic Surgery, Columbia University Medical Center, New York, NY, USA
| | - Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Laurent Perreard
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Fred W Kolling
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - George J Zanazzi
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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21
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Feinberg AP, Levchenko A. Epigenetics as a mediator of plasticity in cancer. Science 2023; 379:eaaw3835. [PMID: 36758093 PMCID: PMC10249049 DOI: 10.1126/science.aaw3835] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 12/22/2022] [Indexed: 02/11/2023]
Abstract
The concept of an epigenetic landscape describing potential cellular fates arising from pluripotent cells, first advanced by Conrad Waddington, has evolved in light of experiments showing nondeterministic outcomes of regulatory processes and mathematical methods for quantifying stochasticity. In this Review, we discuss modern approaches to epigenetic and gene regulation landscapes and the associated ideas of entropy and attractor states, illustrating how their definitions are both more precise and relevant to understanding cancer etiology and the plasticity of cancerous states. We address the interplay between different types of regulatory landscapes and how their changes underlie cancer progression. We also consider the roles of cellular aging and intrinsic and extrinsic stimuli in modulating cellular states and how landscape alterations can be quantitatively mapped onto phenotypic outcomes and thereby used in therapy development.
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Affiliation(s)
- Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University Schools of Medicine, Biomedical Engineering, and Public Health, Baltimore, MD 21205, USA
| | - Andre Levchenko
- Yale Systems Biology Institute and Department of Biomedical Engineering, Yale University, West Haven, CT 06516, USA
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22
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Yin PY, Wang RW, Jing R, Li X, Ma JH, Li KM, Wang H. Research progress on molecular biomarkers of acute myeloid leukemia. Front Oncol 2023; 13:1078556. [PMID: 36824144 PMCID: PMC9941555 DOI: 10.3389/fonc.2023.1078556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common type of adult acute leukemia. The pathophysiology of the disease has been studied intensively at the cellular and molecular levels. At present, cytogenetic markers are an important basis for the early diagnosis, prognostic stratification and treatment of AML. However, with the emergence of new technologies, the detection of other molecular markers, such as gene mutations and epigenetic changes, began to play important roles in evaluating the occurrence and development of diseases. Recent evidence shows that identifying new AML biomarkers contributes to a better understanding of the molecular mechanism of the disease and is essential for AML screening, diagnosis, prognosis monitoring, and individualized treatment response. In this review, we summarized the promising AML biomarkers from four aspects, which contributing to a better understanding of the disease. Of course, it must be soberly aware that we have not listed all biomarkers of AML. Anyway, the biomarkers we mentioned are representative. For example, mutations in TP53, FLT3, and ASXL1 suggest poor prognosis, low remission rate, short survival period, and often require allogeneic hematopoietic stem cell transplantation. The CEBPA double mutation, NPM1 and CBF mutation suggest that the prognosis is good, the remission rate is high, the survival period is long, and the effect of chemotherapy or autotherapy is good. As for other mutations mentioned in the article, they usually predict a moderate prognosis. All in all, we hope it could provide a reference for the precise diagnosis and treatment of AML.
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Affiliation(s)
- Pei-Yuan Yin
- Hematology Department, Yantai Affiliated Hospital, Binzhou Medical University, Yantai, Shandong, China,Department of Blood Supply, Yantai Center Blood Station, Yantai, Shandong, China
| | - Rui-Wen Wang
- Department of Anesthesiology, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, China
| | - Rui Jing
- Hematology Department, Yantai Affiliated Hospital, Binzhou Medical University, Yantai, Shandong, China
| | - Xing Li
- Department of Blood Supply, Yantai Center Blood Station, Yantai, Shandong, China
| | - Jing-Hua Ma
- Department of Science and Education, Yantai Hospital of Traditional Chinese Medicine, Yantai, Shandong, China,*Correspondence: Hua Wang, ; Kai-Min Li, ; Jing-Hua Ma,
| | - Kai-Min Li
- Hematology Department, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, China,*Correspondence: Hua Wang, ; Kai-Min Li, ; Jing-Hua Ma,
| | - Hua Wang
- Hematology Department, Yantai Affiliated Hospital, Binzhou Medical University, Yantai, Shandong, China,*Correspondence: Hua Wang, ; Kai-Min Li, ; Jing-Hua Ma,
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23
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Kayser S, Levis MJ. The clinical impact of the molecular landscape of acute myeloid leukemia. Haematologica 2023; 108:308-320. [PMID: 36722402 PMCID: PMC9890016 DOI: 10.3324/haematol.2022.280801] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Indexed: 02/02/2023] Open
Abstract
Research into the underlying pathogenic mechanisms of acute myeloid leukemia (AML) has led to remarkable advances in our understanding of the disease. Mutations now allow us to explore the enormous diversity among cytogenetically defined subsets of AML, particularly the large subset of cytogenetically normal AML. Despite the progress in unraveling the tumor genome, only a small number of recurrent mutations have been incorporated into risk-stratification schemes and have been proven to be clinically relevant, targetable lesions. The current World Health Organization Classification of myeloid neoplasms and leukemia includes eight AML categories defined by recurrent genetic abnormalities as well as three categories defined by gene mutations. We here discuss the utility of molecular markers in AML in prognostication and treatment decision-making. New therapies based on targetable markers include IDH inhibitors (ivosidenib, enasidenib), venetoclax-based therapy, FLT3 inhibitors (midostaurin, gilteritinib, and quizartinib), gemtuzumab ozogamicin, magrolimab and menin inhibitors.
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Affiliation(s)
- Sabine Kayser
- NCT Trial Center, National Center of Tumor Diseases, German Cancer Research Center (DKFZ), Heidelberg.
| | - Mark J. Levis
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University Baltimore, MD, USA
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24
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Li S. Inferring the Cancer Cellular Epigenome Heterogeneity via DNA Methylation Patterns. Cancer Treat Res 2023; 190:375-393. [PMID: 38113008 DOI: 10.1007/978-3-031-45654-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Tumor cells evolve through space and time, generating genetically and phenotypically diverse cancer cell populations that are continually subjected to the selection pressures of their microenvironment and cancer treatment.
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Affiliation(s)
- Sheng Li
- The Jackson Laboratory for Genomic Medicine and Cancer Center, Farmington, USA.
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25
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Yang C, Tao H, Zhang H, Xia Y, Bai J, Ge G, Li W, Zhang W, Xiao L, Xu Y, Wang Z, Gu Y, Yang H, Liu Y, Geng D. TET2 regulates osteoclastogenesis by modulating autophagy in OVX-induced bone loss. Autophagy 2022; 18:2817-2829. [PMID: 35255774 PMCID: PMC9673923 DOI: 10.1080/15548627.2022.2048432] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Increased bone resorption by osteoclasts after estrogen deficiency is the main cause of postmenopausal osteoporosis. TET2 (tet methylcytosine dioxygenase 2) is a DNA demethylase that regulates cellular function and differentiation potential. Macroautophagy/autophagy maintains cellular homeostasis by recycling unnecessary and damaged organelles. This study revealed that TET2 promoted bone loss in oophorectomized (OVX) mice and that TET2 promoted osteoclast differentiation by regulating autophagy. Tet2 knockdown inhibited autophagy and osteoclast differentiation in vitro. Mechanistically, Tet2 knockdown increased BCL2 (B cell leukemia/lymphoma 2) expression and BCL2 exhibited increased binding to BECN1 and negatively regulated autophagy. Small interfering RNA specific to Bcl2 interfered with BCL2 expression in Tet2-knockdown bone marrow cells/precursors, partially reversing autophagy dysregulation and promoting osteoclast differentiation. Moreover, the LV-shTet2 lentivirus prevented bone loss in OVX mice. In summary, our findings provide evidence that TET2 promotes osteoclast differentiation by inhibiting BCL2 expression and positively regulating BECN1-dependent autophagy.Abbreviations: ACP5/TRAP: acid phosphatase 5, tartrate resistant; ATP6V0D2: ATPase, H+ transporting, lysosomal V0 subunit D2; BCL2: B cell leukemia/lymphoma 2; BECN1: beclin 1, autophagy related; BMs: bone marrow cells; CTSK: cathepsin K; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MMP9: matrix metallopeptidase 9; OVX: oophorectomy; RUNX1: runt related transcription factor 1; SOCS3: suppressor of cytokine signaling 3; SPI1/PU.1: Spi-1 proto-oncogene; TNFSF11/RANKL: tumor necrosis factor (ligand) superfamily, member 11; TET2: tet methylcytosine dioxygenase 2.
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Affiliation(s)
- Chen Yang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Huaqiang Tao
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- CONTACT Jiaxiang Bai Department of Orthopedics, The First Affiliated Hospital of Soochow University, No. 188 Shizi StreetSuzhou, Jiangsu, 215006, China
| | - Haifeng Zhang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Dechun Geng
| | - Yu Xia
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Huilin Yang
| | - Jiaxiang Bai
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Yu Liu Department of Orthopedics, Wuxi Ninth People’s Hospital Affiliated to Soochow University, Wuxi, Jiangsu214062, China
| | - Gaoran Ge
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Wenming Li
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Wei Zhang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Long Xiao
- Department of Orthopedics, Zhangjiagang Tcm Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, China
| | - Yaozeng Xu
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Zhirong Wang
- Department of Orthopedics, Zhangjiagang Tcm Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, China
| | - Ye Gu
- Department of Orthopedics, Central Laboratory, Changshu Hospital Affiliated to Soochow University, First People’s Hospital of Changshu City, Changshu, Jiangsu, China
| | - Huilin Yang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yu Liu
- Department of Orthopedics, Wuxi Ninth People’s Hospital Affiliated to Soochow University, Wuxi, Jiangsu, China
| | - Dechun Geng
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Orthopedics, Central Laboratory, Changshu Hospital Affiliated to Soochow University, First People’s Hospital of Changshu City, Changshu, Jiangsu, China
- Dechun Geng
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26
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Wang T, Hua H, Wang Z, Wang B, Cao L, Qin W, Wu P, Cai X, Chao H, Lu X. Frequency and clinical impact of WT1 mutations in the context of CEBPA-mutated acute myeloid leukemia. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:994-1002. [PMID: 36066283 DOI: 10.1080/16078454.2022.2103964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Several studies have confirmed that mutations in the Wilms tumor 1 (WT1) gene occur in adult acute myeloid leukemia (AML). However, few data are available regarding the incidence of WT1 mutations in CEBPAmut AML and their impact. METHODS We retrospectively analyzed the frequency and clinical impact of WT1 mutations in 220 newly diagnosed AML patients with CEBPA mutations(CEBPAmut). Chromosome karyotype analysis was performed by R or G banding method and further confirmed either by fluorescence in situ hybridization (FISH) and/or by multiple reverse transcription polymerase chain reaction (multiple RT-PCR). Mutations were detected with a panel of 112mutational genes using next-generation sequencing (NGS). RESULTS Overall, 30 WT1 mutations were detected in 29 of the 220 CEBPAmut AML patients (13.18%) screened. These mutations clustered overwhelmingly in exon 7 (n=16). WT1 mutations were found to be significantly more frequent in AML patients with double-mutated CEBPA (CEBPAdm) than in AML patients with single-mutated CEBPA (17.36%vs. 8.08%, P = 0.043). Among WT1-mutated patients, the most common co-mutation was FLT3-ITD (n = 7, 24.14%), followed by NRAS (n = 5, 17.24%), CSF3R (n = 4, 13.79%), GATA2 (n = 4, 13.79%), and KIT (n = 4, 13.79%). The most frequent functional pathway was signaling pathways inas many as 62.07% of cases. Notably,the concomitant mutations in epigenetic regulatorswere inversely correlated with WT1 mutations(P = 0.003). CEBPAdm AML patients with WT1 mutations had inferior relapse-free survival, event-free survival and overall survival compared with patients CEBPAdm AML without WT1 mutations (P = 0.002, 0.004, and 0.010, respectively). CONCLUSION Our data showed that WT1 mutations are frequently identified in CEBPAmut AML, especially in CEBPAdm AML. CEBPAmut AML patients with WT1 mutations show distinct spectrum of comutations. In the context of CEBPAdm AML, WT1 mutations predict a poor prognosis.
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Affiliation(s)
- Ting Wang
- Department of Hematology, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, People's Republic of China
| | - Haiying Hua
- Department of Hematology, Wuxi Third people's hospital, Wuxi, People's Republic of China
| | - Zheng Wang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China.,Suzhou jsuniwell medical laboratory, Suzhou, People's Republic of China
| | - Biao Wang
- Department of Hematology, The Third Affiliated Hospital of Soochow University, Changzhou, People's Republic of China
| | - Liujun Cao
- Department of Hematology, Affiliated Jintan People's Hospital of Jiangsu University, Changzhou, People's Republic of China
| | - Wei Qin
- Department of Hematology, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, People's Republic of China
| | - Pin Wu
- Department of Hematology, Wuxi Second people's hospital, Wuxi, People's Republic of China
| | - Xiaohui Cai
- Department of Hematology, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, People's Republic of China
| | - Hongying Chao
- Department of Hematology, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, People's Republic of China
| | - XuZhang Lu
- Department of Hematology, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, People's Republic of China
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Shikonin as a WT1 Inhibitor Promotes Promyeloid Leukemia Cell Differentiation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238264. [PMID: 36500358 PMCID: PMC9735585 DOI: 10.3390/molecules27238264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
This study aims to observe the differentiating effect of shikonin on Wilms' tumor 1 (WT1)-positive HL-60 cells and investigate the fate of the differentiated leukemia cells. WT1 overexpression unaffected cell viability but promoted resistance to H2O2-induced DNA injury and cell apoptosis. The binding of shikonin to the WT1 protein was confirmed by molecular docking and drug affinity reaction target stability (DARTS). Shikonin at the non-cytotoxic concentration could decrease the WT1 protein and simultaneously reduced the CD34 protein and increased the CD11b protein in a dose-dependent manner in normal HL-60 cells but not in WT1-overexpressed HL-60 cells. Shikonin unaffected HL-60 cell viability in 48 h. However, it lasted for 10 days; could attenuate cell proliferation, mitochondrial membrane potential (MMP), and self-renewal; prevent the cell cycle; promote cell apoptosis. In a mouse leukemia model, shikonin could decrease the WT1 protein to prevent leukemia development in a dose-dependent manner. In this study, we also confirmed preliminarily the protein-protein interactions between WT1 and CD34 in molecular docking and CO-IP assay. Our results suggest that: 1. shikonin can down-regulate the WT1 protein level for leukemia differentiation therapy, and 2. the interaction between WT1 and CD34 proteins may be responsible for granulocyte/monocyte immaturity in HL-60 cells.
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Shi X, Zhou H, Wei J, Mo W, Li Q, Lv X. The signaling pathways and therapeutic potential of itaconate to alleviate inflammation and oxidative stress in inflammatory diseases. Redox Biol 2022; 58:102553. [PMID: 36459716 PMCID: PMC9713374 DOI: 10.1016/j.redox.2022.102553] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Endogenous small molecules are metabolic regulators of cell function. Itaconate is a key molecule that accumulates in cells when the Krebs cycle is disrupted. Itaconate is derived from cis-aconitate decarboxylation by cis-aconitate decarboxylase (ACOD1) in the mitochondrial matrix and is also known as immune-responsive gene 1 (IRG1). Studies have demonstrated that itaconate plays an important role in regulating signal transduction and posttranslational modification through its immunoregulatory activities. Itaconate is also an important bridge among metabolism, inflammation, oxidative stress, and the immune response. This review summarizes the structural characteristics and classical pathways of itaconate, its derivatives, and the compounds that release itaconate. Here, the mechanisms of itaconate action, including its transcriptional regulation of ATF3/IκBζ axis and type I IFN, its protein modification regulation of KEAP1, inflammasome, JAK1/STAT6 pathway, TET2, and TFEB, and succinate dehydrogenase and glycolytic enzyme metabolic action, are presented. Moreover, the roles of itaconate in diseases related to inflammation and oxidative stress induced by autoimmune responses, viruses, sepsis and IRI are discussed in this review. We hope that the information provided in this review will help increase the understanding of cellular immune metabolism and improve the clinical treatment of diseases related to inflammation and oxidative stress.
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MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia. Nat Commun 2022; 13:6524. [PMID: 36316347 PMCID: PMC9622910 DOI: 10.1038/s41467-022-34211-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
DNMT3A and IDH1/2 mutations combinatorically regulate the transcriptome and the epigenome in acute myeloid leukemia; yet the mechanisms of this interplay are unknown. Using a systems approach within topologically associating domains, we find that genes with significant expression-methylation correlations are enriched in signaling and metabolic pathways. The common denominator across these methylation-regulated genes is the density in MIR retrotransposons of their introns. Moreover, a discrete number of CpGs overlapping enhancers are responsible for regulating most of these genes. Established mouse models recapitulate the dependency of MIR-rich genes on the balanced expression of epigenetic modifiers, while projection of leukemic profiles onto normal hematopoiesis ones further consolidates the dependencies of methylation-regulated genes on MIRs. Collectively, MIR elements on genes and enhancers are susceptible to changes in DNA methylation activity and explain the cooperativity of proteins in this pathway in normal and malignant hematopoiesis.
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30
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Role of TET dioxygenases in the regulation of both normal and pathological hematopoiesis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:294. [PMID: 36203205 PMCID: PMC9540719 DOI: 10.1186/s13046-022-02496-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
Abstract
The family of ten-eleven translocation dioxygenases (TETs) consists of TET1, TET2, and TET3. Although all TETs are expressed in hematopoietic tissues, only TET2 is commonly found to be mutated in age-related clonal hematopoiesis and hematopoietic malignancies. TET2 mutation causes abnormal epigenetic landscape changes and results in multiple stages of lineage commitment/differentiation defects as well as genetic instability in hematopoietic stem/progenitor cells (HSPCs). TET2 mutations are founder mutations (first hits) in approximately 40–50% of cases of TET2-mutant (TET2MT) hematopoietic malignancies and are later hits in the remaining cases. In both situations, TET2MT collaborates with co-occurring mutations to promote malignant transformation. In TET2MT tumor cells, TET1 and TET3 partially compensate for TET2 activity and contribute to the pathogenesis of TET2MT hematopoietic malignancies. Here we summarize the most recent research on TETs in regulating of both normal and pathogenic hematopoiesis. We review the concomitant mutations and aberrant signals in TET2MT malignancies. We also discuss the molecular mechanisms by which concomitant mutations and aberrant signals determine lineage commitment in HSPCs and the identity of hematopoietic malignancies. Finally, we discuss potential strategies to treat TET2MT hematopoietic malignancies, including reverting the methylation state of TET2 target genes and targeting the concomitant mutations and aberrant signals.
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Song H, Liu Y, Tan Y, Zhang Y, Jin W, Chen L, Wu S, Yan J, Li J, Chen Z, Chen S, Wang K. Recurrent noncoding somatic and germline WT1 variants converge to disrupt MYB binding in acute promyelocytic leukemia. Blood 2022; 140:1132-1144. [PMID: 35653587 PMCID: PMC9461475 DOI: 10.1182/blood.2021014945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Genetic alternations can occur at noncoding regions, but how they contribute to cancer pathogenesis is poorly understood. Here, we established a mutational landscape of cis-regulatory regions (CREs) in acute promyelocytic leukemia (APL) based on whole-genome sequencing analysis of paired tumor and germline samples from 24 patients and epigenetic profiling of 16 patients. Mutations occurring in CREs occur preferentially in active enhancers bound by the complex of master transcription factors in APL. Among significantly enriched mutated CREs, we found a recurrently mutated region located within the third intron of WT1, an essential regulator of normal and malignant hematopoiesis. Focusing on noncoding mutations within this WT1 intron, an analysis on 169 APL patients revealed that somatic mutations were clustered into a focal hotspot region, including one site identified as a germline polymorphism contributing to APL risk. Significantly decreased WT1 expression was observed in APL patients bearing somatic and/or germline noncoding WT1 variants. Furthermore, biallelic WT1 inactivation was recurrently found in APL patients with noncoding WT1 variants, which resulted in the complete loss of WT1. The high incidence of biallelic inactivation suggested the tumor suppressor activity of WT1 in APL. Mechanistically, noncoding WT1 variants disrupted MYB binding on chromatin and suppressed the enhancer activity and WT1 expression through destroying the chromatin looping formation. Our study highlights the important role of noncoding variants in the leukemogenesis of APL.
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Affiliation(s)
- Huan Song
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yabin Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shishuang Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinsong Yan
- Department of Hematology, the Second Hospital of Dalian Medical University, Dalian, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
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32
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Joshi K, Liu S, Breslin S J P, Zhang J. Mechanisms that regulate the activities of TET proteins. Cell Mol Life Sci 2022; 79:363. [PMID: 35705880 DOI: 10.1007/s00018-022-04396-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 02/08/2023]
Abstract
The ten-eleven translocation (TET) family of dioxygenases consists of three members, TET1, TET2, and TET3. All three TET enzymes have Fe+2 and α-ketoglutarate (α-KG)-dependent dioxygenase activities, catalyzing the 1st step of DNA demethylation by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and further oxidize 5hmC to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Gene knockout studies demonstrated that all three TET proteins are involved in the regulation of fetal organ generation during embryonic development and normal tissue generation postnatally. TET proteins play such roles by regulating the expression of key differentiation and fate-determining genes via (1) enzymatic activity-dependent DNA methylation of the promoters and enhancers of target genes; and (2) enzymatic activity-independent regulation of histone modification. Interacting partner proteins and post-translational regulatory mechanisms regulate the activities of TET proteins. Mutations and dysregulation of TET proteins are involved in the pathogenesis of human diseases, specifically cancers. Here, we summarize the research on the interaction partners and post-translational modifications of TET proteins. We also discuss the molecular mechanisms by which these partner proteins and modifications regulate TET functioning and target gene expression. Such information will help in the design of medications useful for targeted therapy of TET-mutant-related diseases.
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Affiliation(s)
- Kanak Joshi
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Shanhui Liu
- School of Life Sciences, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Peter Breslin S J
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.,Departments of Molecular/Cellular Physiology and Biology, Loyola University Medical Center and Loyola University Chicago, Chicago, IL, 60660, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA. .,Departments of Pathology and Radiation Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA.
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33
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Banella C, Catalano G, Travaglini S, Pelosi E, Ottone T, Zaza A, Guerrera G, Angelini DF, Niscola P, Divona M, Battistini L, Screnci M, Ammatuna E, Testa U, Nervi C, Voso MT, Noguera NI. Ascorbate Plus Buformin in AML: A Metabolic Targeted Treatment. Cancers (Basel) 2022; 14:cancers14102565. [PMID: 35626170 PMCID: PMC9139619 DOI: 10.3390/cancers14102565] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Acute Myeloid Leukemias (AMLs) are rapidly progressive clonal neoplastic diseases. The overall 5-year survival rate is very poor: less than 5% in older patients aged over 65 years old. Elderly AML patients are often “unfit” for intensive chemotherapy, further highlighting the need of highly effective, well-tolerated new treatment options for AMLs. Growing evidence indicates that AML blasts feature a highly diverse and flexible metabolism consistent with the aggressiveness of the disease. Based on these evidences, we targeted the metabolic peculiarity and plasticity of AML cells with an association of ascorbate, which causes oxidative stress and interferes with hexokinase activity, and buformin, which completely shuts down mitochondrial contributions in ATP production. The ascorbate–buformin combination could be an innovative therapeutic option for elderly AML patients that are resistant to therapy. Abstract In the present study, we characterized the metabolic background of different Acute Myeloid Leukemias’ (AMLs) cells and described a heterogeneous and highly flexible energetic metabolism. Using the Seahorse XF Agilent, we compared the metabolism of normal hematopoietic progenitors with that of primary AML blasts and five different AML cell lines. We assessed the efficacy and mechanism of action of the association of high doses of ascorbate, a powerful oxidant, with the metabolic inhibitor buformin, which inhibits mitochondrial complex I and completely shuts down mitochondrial contributions in ATP production. Primary blasts from seventeen AML patients, assayed for annexin V and live/dead exclusion by flow cytometry, showed an increase in the apoptotic effect using the drug combination, as compared with ascorbate alone. We show that ascorbate inhibits glycolysis through interfering with HK1/2 and GLUT1 functions in hematopoietic cells. Ascorbate combined with buformin decreases mitochondrial respiration and ATP production and downregulates glycolysis, enhancing the apoptotic effect of ascorbate in primary blasts from AMLs and sparing normal CD34+ bone marrow progenitors. In conclusion, our data have therapeutic implications especially in fragile patients since both agents have an excellent safety profile, and the data also support the clinical evaluation of ascorbate–buformin in association with different mechanism drugs for the treatment of refractory/relapsing AML patients with no other therapeutic options.
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Affiliation(s)
- Cristina Banella
- Neurooncoemtology Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (C.B.); (G.C.); (S.T.); (T.O.); (A.Z.)
- Department of Health Sciences, Meyer Children’s University Hospital, 50139 Florence, Italy
| | - Gianfranco Catalano
- Neurooncoemtology Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (C.B.); (G.C.); (S.T.); (T.O.); (A.Z.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Serena Travaglini
- Neurooncoemtology Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (C.B.); (G.C.); (S.T.); (T.O.); (A.Z.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Elvira Pelosi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (E.P.); (U.T.)
| | - Tiziana Ottone
- Neurooncoemtology Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (C.B.); (G.C.); (S.T.); (T.O.); (A.Z.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Alessandra Zaza
- Neurooncoemtology Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (C.B.); (G.C.); (S.T.); (T.O.); (A.Z.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Gisella Guerrera
- Neuroimmunology and Flow Cytometry Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (G.G.); (D.F.A.); (L.B.)
| | - Daniela Francesca Angelini
- Neuroimmunology and Flow Cytometry Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (G.G.); (D.F.A.); (L.B.)
| | - Pasquale Niscola
- Hematology Unit, Saint’ Eugenio Hospital, University of Rome Tor Vergata, 00144 Rome, Italy;
| | | | - Luca Battistini
- Neuroimmunology and Flow Cytometry Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (G.G.); (D.F.A.); (L.B.)
| | - Maria Screnci
- Banca Regionale Sangue Cordone Ombelicale UOC Immunoematologia e Medicina Trasfusionale, Policlinico Umberto I, 00161 Roma, Italy;
| | - Emanuele Ammatuna
- Department of Hematology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Ugo Testa
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (E.P.); (U.T.)
| | - Clara Nervi
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma La Sapienza, 04100 Latina, Italy;
| | - Maria Teresa Voso
- Neurooncoemtology Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (C.B.); (G.C.); (S.T.); (T.O.); (A.Z.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (M.T.V.); (N.I.N.); Tel.: +39-06-501-703-225 (N.I.N.)
| | - Nelida Ines Noguera
- Neurooncoemtology Units, Santa Lucia Foundation, I.R.C.C.S., 00143 Rome, Italy; (C.B.); (G.C.); (S.T.); (T.O.); (A.Z.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (M.T.V.); (N.I.N.); Tel.: +39-06-501-703-225 (N.I.N.)
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Kirschner KM, Scholz H. WT1 in Adipose Tissue: From Development to Adult Physiology. Front Cell Dev Biol 2022; 10:854120. [PMID: 35372335 PMCID: PMC8965737 DOI: 10.3389/fcell.2022.854120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/28/2022] [Indexed: 11/30/2022] Open
Abstract
Much of the fascination of the Wilms tumor protein (WT1) emanates from its unique roles in development and disease. Ubiquitous Wt1 deletion in adult mice causes multiple organ failure including a reduction of body fat. WT1 is expressed in fat cell progenitors in visceral white adipose tissue (WAT) but detected neither in energy storing subcutaneous WAT nor in heat producing brown adipose tissue (BAT). Our recent findings indicate that WT1 represses thermogenic genes and maintains the white adipose identity of visceral fat. Wt1 heterozygosity in mice is associated with molecular and morphological signs of browning including elevated levels of uncoupling protein 1 (UCP1) in epididymal WAT. Compared to their wild-type littermates, Wt1 heterozygous mice exhibit significantly improved whole-body glucose tolerance and alleviated hepatic steatosis under high-fat diet. Partial protection of heterozygous Wt1 knockout mice against metabolic dysfunction is presumably related to browning of their epididymal WAT. In the light of recent advancements, this article reviews the role of WT1 in the development of visceral WAT and its supposed function as a regulator of white adipose identity.
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35
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Itaconate inhibits TET DNA dioxygenases to dampen inflammatory responses. Nat Cell Biol 2022; 24:353-363. [DOI: 10.1038/s41556-022-00853-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/26/2022] [Indexed: 12/19/2022]
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36
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Mondello P, Ansell SM, Nowakowski GS. Immune Epigenetic Crosstalk Between Malignant B Cells and the Tumor Microenvironment in B Cell Lymphoma. Front Genet 2022; 13:826594. [PMID: 35237302 PMCID: PMC8883034 DOI: 10.3389/fgene.2022.826594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/24/2022] [Indexed: 12/22/2022] Open
Abstract
Epigenetic reprogramming is a hallmark of lymphomagenesis, however its role in reshaping the tumor microenvironment is still not well understood. Here we review the most common chromatin modifier mutations in B cell lymphoma and their effect on B cells as well as on T cell landscape. We will also discuss precision therapy strategies to reverse their aberrant signaling by targeting mutated proteins or counterbalance epigenetic mechanisms.
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37
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Dissecting TET2 Regulatory Networks in Blood Differentiation and Cancer. Cancers (Basel) 2022; 14:cancers14030830. [PMID: 35159097 PMCID: PMC8834528 DOI: 10.3390/cancers14030830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Bone marrow disorders such as leukemia and myelodysplastic syndromes are characterized by abnormal healthy blood cells production and function. Uncontrolled growth and impaired differentiation of white blood cells hinder the correct development of healthy cells in the bone marrow. One of the most frequent alterations that appear to initiate this deregulation and persist in leukemia patients are mutations in epigenetic regulators such as TET2. This review summarizes the latest molecular findings regarding TET2 functions in hematopoietic cells and their potential implications in blood cancer origin and evolution. Our goal was to encompass and interlink up-to-date discoveries of the convoluted TET2 functional network to provide a more precise overview of the leukemic burden of this protein. Abstract Cytosine methylation (5mC) of CpG is the major epigenetic modification of mammalian DNA, playing essential roles during development and cancer. Although DNA methylation is generally associated with transcriptional repression, its role in gene regulation during cell fate decisions remains poorly understood. DNA demethylation can be either passive or active when initiated by TET dioxygenases. During active demethylation, transcription factors (TFs) recruit TET enzymes (TET1, 2, and 3) to specific gene regulatory regions to first catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and subsequently to higher oxidized cytosine derivatives. Only TET2 is frequently mutated in the hematopoietic system from the three TET family members. These mutations initially lead to the hematopoietic stem cells (HSCs) compartment expansion, eventually evolving to give rise to a wide range of blood malignancies. This review focuses on recent advances in characterizing the main TET2-mediated molecular mechanisms that activate aberrant transcriptional programs in blood cancer onset and development. In addition, we discuss some of the key outstanding questions in the field.
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Pronier E, Imanci A, Selimoglu-Buet D, Badaoui B, Itzykson R, Roger T, Jego C, Naimo A, Francillette M, Breckler M, Wagner-Ballon O, Figueroa ME, Aglave M, Gautheret D, Porteu F, Bernard OA, Vainchenker W, Delhommeau F, Solary E, Droin NM. Macrophage migration inhibitory factor is overproduced through EGR1 in TET2 low resting monocytes. Commun Biol 2022; 5:110. [PMID: 35115654 PMCID: PMC8814058 DOI: 10.1038/s42003-022-03057-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 01/06/2022] [Indexed: 12/14/2022] Open
Abstract
Somatic mutation in TET2 gene is one of the most common clonal genetic events detected in age-related clonal hematopoiesis as well as in chronic myelomonocytic leukemia (CMML). In addition to being a pre-malignant state, TET2 mutated clones are associated with an increased risk of death from cardiovascular disease, which could involve cytokine/chemokine overproduction by monocytic cells. Here, we show in mice and in human cells that, in the absence of any inflammatory challenge, TET2 downregulation promotes the production of MIF (macrophage migration inhibitory factor), a pivotal mediator of atherosclerotic lesion formation. In healthy monocytes, TET2 is recruited to MIF promoter and interacts with the transcription factor EGR1 and histone deacetylases. Disruption of these interactions as a consequence of TET2-decreased expression favors EGR1-driven transcription of MIF gene and its secretion. MIF favors monocytic differentiation of myeloid progenitors. These results designate MIF as a chronically overproduced chemokine and a potential therapeutic target in patients with clonal TET2 downregulation in myeloid cells. To improve our understanding of the pathological role of TET2 mutations, Pronier, Imanci et al. use mice and human cells to show that TET2 downregulation promotes the production of macrophage migration inhibitory factor (MIF). In addition they show that whilst TET2 is recruited to the MIF promoter in healthy monocytes, decreased TET2 expression results in chronic overproduction of MIF - suggesting that MIF signaling could therefore constitute a potential therapeutic target for conditions associated with TET2 mutations.
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Affiliation(s)
- Elodie Pronier
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Owkin Lab, Owkin, Inc., New York, NY, 10003, USA
| | - Aygun Imanci
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - Dorothée Selimoglu-Buet
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - Bouchra Badaoui
- AP-HP, Hôpitaux Universitaires Henri-Mondor, Département d'Hématologie et Immunologie Biologiques, 94000, Créteil, France
| | - Raphael Itzykson
- AP-HP, Service Hématologie Adultes, Hôpital Saint-Louis, 75010, Paris, France
| | - Thierry Roger
- Infectious Disease Service, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, 1011, Lausanne, Switzerland
| | - Chloé Jego
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - Audrey Naimo
- INSERM US23, CNRS UMS 3655, AMMICa, Genomic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Maëla Francillette
- INSERM US23, CNRS UMS 3655, AMMICa, Genomic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Marie Breckler
- INSERM US23, CNRS UMS 3655, AMMICa, Genomic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Orianne Wagner-Ballon
- AP-HP, Hôpitaux Universitaires Henri-Mondor, Département d'Hématologie et Immunologie Biologiques, 94000, Créteil, France.,Université Paris Est Créteil, INSERM, IMRB, Equipe 9, 94010, Créteil, France
| | - Maria E Figueroa
- Human Genetics, University of Miami Miller School of Medicine, 33136, Miami, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 33136, Miami, USA
| | - Marine Aglave
- INSERM US23, CNRS UMS 3655, AMMICa, Bioinformatic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Daniel Gautheret
- INSERM US23, CNRS UMS 3655, AMMICa, Bioinformatic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Françoise Porteu
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - Olivier A Bernard
- Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France.,INSERM U1170, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - William Vainchenker
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - François Delhommeau
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France.,AP-HP, Sorbonne Université, Hôpital Saint-Antoine, Service d'Hématologie et Immunologie Biologique, 75012, Paris, France
| | - Eric Solary
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France.,Hematology department, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Nathalie M Droin
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France. .,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France. .,INSERM US23, CNRS UMS 3655, AMMICa, Genomic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France.
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Chen X, Zhou W, Song RH, Liu S, Wang S, Chen Y, Gao C, He C, Xiao J, Zhang L, Wang T, Liu P, Duan K, Cheng Z, Zhang C, Zhang J, Sun Y, Jackson F, Lan F, Liu Y, Xu Y, Wong JJL, Wang P, Yang H, Xiong Y, Chen T, Li Y, Ye D. Tumor suppressor CEBPA interacts with and inhibits DNMT3A activity. SCIENCE ADVANCES 2022; 8:eabl5220. [PMID: 35080973 PMCID: PMC8791617 DOI: 10.1126/sciadv.abl5220] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
DNA methyltransferases (DNMTs) catalyze DNA methylation, and their functions in mammalian embryonic development and diseases including cancer have been extensively studied. However, regulation of DNMTs remains under study. Here, we show that CCAAT/enhancer binding protein α (CEBPA) interacts with the long splice isoform DNMT3A, but not the short isoform DNMT3A2. CEBPA, by interacting with DNMT3A N-terminus, blocks DNMT3A from accessing DNA substrate and thereby inhibits its activity. Recurrent tumor-associated CEBPA mutations, such as preleukemic CEBPAN321D mutation, which is particularly potent in causing AML with high mortality, disrupt DNMT3A association and cause aberrant DNA methylation, notably hypermethylation of PRC2 target genes. Consequently, leukemia cells with the CEBPAN321D mutation are hypersensitive to hypomethylation agents. Our results provide insights into the functional difference between DNMT3A isoforms and the regulation of de novo DNA methylation at specific loci in the genome. Our study also suggests a therapeutic strategy for the treatment of CEBPA-mutated leukemia with DNA-hypomethylating agents.
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Affiliation(s)
- Xiufei Chen
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Target Discovery Institute, NDM Research Building, Oxford Ludwig Institute of Cancer Research, Oxford University, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Wenjie Zhou
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ren-Hua Song
- Epigenetics and RNA Biology Program, Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Shuang Liu
- MOE Key Laboratory of Model Animals for Disease Study, Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Chemistry and Biomedicine Innovation Center (ChemBIC), Model Animal Research Center, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Shu Wang
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yujia Chen
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chao Gao
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chenxi He
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jianxiong Xiao
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lei Zhang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Tianxiang Wang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Peng Liu
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kunlong Duan
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhouli Cheng
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chen Zhang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jinye Zhang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yiping Sun
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Felix Jackson
- Department of Computer Science, University of Oxford, 15 Parks Rd, Oxford OX1 3QD, UK
| | - Fei Lan
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanhui Xu
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Justin Jong-Leong Wong
- Epigenetics and RNA Biology Program, Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Pu Wang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hui Yang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Tong Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
- Corresponding author. (T.C.); (Yan Li); (D.Y.)
| | - Yan Li
- MOE Key Laboratory of Model Animals for Disease Study, Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Chemistry and Biomedicine Innovation Center (ChemBIC), Model Animal Research Center, Nanjing University Medical School, Nanjing University, Nanjing, China
- Corresponding author. (T.C.); (Yan Li); (D.Y.)
| | - Dan Ye
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Corresponding author. (T.C.); (Yan Li); (D.Y.)
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Acquired WT1 mutations contribute to relapse of NPM1-mutated acute myeloid leukemia following allogeneic hematopoietic stem cell transplant. Bone Marrow Transplant 2022; 57:370-376. [PMID: 34992253 DOI: 10.1038/s41409-021-01538-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/08/2021] [Accepted: 11/19/2021] [Indexed: 11/08/2022]
Abstract
The role of WT1 protein in hematopoiesis and leukemogenesisis incompletely elucidated. WT1 overexpression is common in acute myeloid leukemia (AML); however, WT1 mutations occur in only about 10% of cases, with increasing incidence in the setting of relapse. In this study, we investigated the clinical and molecular characteristics of WT1 mutations in NPM1-mutated AML, to enhance our understanding of the biology and potential therapeutic implications of WT1 mutations. Our study cohort included 67 patients with NPM1 mutated AML and a median follow-up of 13.7 months. WT1 mutations were identified in 7% (n = 5) of patients at the time of initial diagnosis. WT1 mutant clones were presumed to be present as co-dominant clones in 3/5 and in subclonal populations in 2/5 cases based on variant allelic frequency (VAF) when compared with NPM1 mutation VAF. All WT1 mutations became undetectable at time of MRD-negative (NPM1-wild type) remission. None of these patients experienced relapse at the time of last follow-up (median, 15 months; range, 4.5-20.2 months). A total of 15/67 (22%) patients relapsed; among these patient, four (27%) relapsed with WT1 mutant AML. Three of four patients had undergone allogeneic hematopoietic stem cell transplantation (HSCT). None of these patients had detectable WT1 mutations at the time of initial diagnosis. WT1 mutations were presumed clonal in two cases and subclonal in the other two cases, based on VAF. Our results indicate that WT1 mutations contribute to relapse in NPM1 mutated AML, especially in the setting of HSCT. These findings suggest that emerging WT1 mutations may serve as a conduit for relapse in NPM1-mutated AML, and that sequential molecular profiling to evaluate potential emergent WT1 mutations during surveillance and particularly at relapse likely has prognostic value in patients with NPM1 mutated AML.
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Xu H, Wen Y, Jin R, Chen H. Epigenetic modifications and targeted therapy in pediatric acute myeloid leukemia. Front Pediatr 2022; 10:975819. [PMID: 36147798 PMCID: PMC9485478 DOI: 10.3389/fped.2022.975819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/10/2022] [Indexed: 11/26/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematological malignancy resulting from the genetic alterations and epigenetic dysregulations of the hematopoietic progenitor cells. One-third of children with AML remain at risk of relapse even though outcomes have improved in recent decades. Epigenetic dysregulations have been identified to play a significant role during myeloid leukemogenesis. In contrast to genetic changes, epigenetic modifications are typically reversible, opening the door to the development of epigenetic targeted therapy. In this review, we provide an overview of the landscape of epigenetic alterations and describe the current progress that has been made in epigenetic targeted therapy, and pay close attention to the potential value of epigenetic abnormalities in the precision and combinational therapy of pediatric AML.
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Affiliation(s)
- Huan Xu
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxi Wen
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Runming Jin
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chen
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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42
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Jahn N, Jahn E, Saadati M, Bullinger L, Larson RA, Ottone T, Amadori S, Prior TW, Brandwein JM, Appelbaum FR, Medeiros BC, Tallman MS, Ehninger G, Heuser M, Ganser A, Pallaud C, Gathmann I, Krzykalla J, Benner A, Bloomfield CD, Thiede C, Stone RM, Döhner H, Döhner K. Genomic landscape of patients with FLT3-mutated acute myeloid leukemia (AML) treated within the CALGB 10603/RATIFY trial. Leukemia 2022; 36:2218-2227. [PMID: 35922444 PMCID: PMC9417991 DOI: 10.1038/s41375-022-01650-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 06/22/2022] [Accepted: 07/04/2022] [Indexed: 02/02/2023]
Abstract
The aim of this study was to characterize the mutational landscape of patients with FLT3-mutated acute myeloid leukemia (AML) treated within the randomized CALGB 10603/RATIFY trial evaluating intensive chemotherapy plus the multi-kinase inhibitor midostaurin versus placebo. We performed sequencing of 262 genes in 475 patients: mutations occurring concurrently with the FLT3-mutation were most frequent in NPM1 (61%), DNMT3A (39%), WT1 (21%), TET2 (12%), NRAS (11%), RUNX1 (11%), PTPN11 (10%), and ASXL1 (8%) genes. To assess effects of clinical and genetic features and their possible interactions, we fitted random survival forests and interpreted the resulting variable importance. Highest prognostic impact was found for WT1 and NPM1 mutations, followed by white blood cell count, FLT3 mutation type (internal tandem duplications vs. tyrosine kinase domain mutations), treatment (midostaurin vs. placebo), ASXL1 mutation, and ECOG performance status. When evaluating two-fold variable combinations the most striking effects were found for WT1:NPM1 (with NPM1 mutation abrogating the negative effect of WT1 mutation), and for WT1:treatment (with midostaurin exerting a beneficial effect in WT1-mutated AML). This targeted gene sequencing study provides important, novel insights into the genomic background of FLT3-mutated AML including the prognostic impact of co-mutations, specific gene-gene interactions, and possible treatment effects of midostaurin.
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Affiliation(s)
- Nikolaus Jahn
- grid.410712.10000 0004 0473 882XDepartment of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Ekaterina Jahn
- grid.410712.10000 0004 0473 882XDepartment of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | | | - Lars Bullinger
- grid.6363.00000 0001 2218 4662Department of Hematology, Oncology and Tumor Immunology, Charité University, Berlin, Germany
| | - Richard A. Larson
- grid.170205.10000 0004 1936 7822Department of Medicine and Comprehensive Cancer Center, University of Chicago, Chicago, IL USA
| | - Tiziana Ottone
- grid.6530.00000 0001 2300 0941Department of Biomedicine and Prevention, University Tor Vergata, Rome, Italy ,grid.414603.4Santa Lucia Foundation, Neuro-Oncohematology, I.R.C.C.S., Rome, Italy
| | - Sergio Amadori
- grid.6530.00000 0001 2300 0941Department of Biomedicine and Prevention, University Tor Vergata, Rome, Italy
| | - Thomas W. Prior
- grid.67105.350000 0001 2164 3847Case Western Reserve University, Cleveland, OH USA
| | - Joseph M. Brandwein
- grid.17089.370000 0001 2190 316XDepartment of Medicine, University of Alberta, Edmonton, AB Canada
| | - Frederick R. Appelbaum
- grid.270240.30000 0001 2180 1622Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Bruno C. Medeiros
- grid.168010.e0000000419368956Division of Hematology, Stanford Comprehensive Cancer Center, Stanford University, Stanford, CA USA
| | - Martin S. Tallman
- grid.51462.340000 0001 2171 9952Division of Hematologic Malignancies, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Gerhard Ehninger
- grid.412282.f0000 0001 1091 2917Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - Michael Heuser
- grid.10423.340000 0000 9529 9877Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- grid.10423.340000 0000 9529 9877Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Celine Pallaud
- grid.419481.10000 0001 1515 9979Novartis Pharmaceuticals, Basel, Switzerland
| | - Insa Gathmann
- grid.419481.10000 0001 1515 9979Novartis Pharmaceuticals, Basel, Switzerland
| | - Julia Krzykalla
- grid.7497.d0000 0004 0492 0584Division of Biostatistics, German Cancer Research Center Heidelberg, Heidelberg, Germany
| | - Axel Benner
- grid.7497.d0000 0004 0492 0584Division of Biostatistics, German Cancer Research Center Heidelberg, Heidelberg, Germany
| | - Clara D. Bloomfield
- grid.261331.40000 0001 2285 7943The Ohio State University Comprehensive Cancer Center, Columbus, OH USA
| | - Christian Thiede
- grid.412282.f0000 0001 1091 2917Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus der TU Dresden, Dresden, Germany
| | - Richard M. Stone
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber/Partners CancerCare, Boston, MA USA
| | - Hartmut Döhner
- grid.410712.10000 0004 0473 882XDepartment of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Konstanze Döhner
- grid.410712.10000 0004 0473 882XDepartment of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
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43
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Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:239-267. [DOI: 10.1007/978-3-031-11454-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Mouse Models of Frequently Mutated Genes in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13246192. [PMID: 34944812 PMCID: PMC8699817 DOI: 10.3390/cancers13246192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 01/19/2023] Open
Abstract
Acute myeloid leukemia is a clinically and biologically heterogeneous blood cancer with variable prognosis and response to conventional therapies. Comprehensive sequencing enabled the discovery of recurrent mutations and chromosomal aberrations in AML. Mouse models are essential to study the biological function of these genes and to identify relevant drug targets. This comprehensive review describes the evidence currently available from mouse models for the leukemogenic function of mutations in seven functional gene groups: cell signaling genes, epigenetic modifier genes, nucleophosmin 1 (NPM1), transcription factors, tumor suppressors, spliceosome genes, and cohesin complex genes. Additionally, we provide a synergy map of frequently cooperating mutations in AML development and correlate prognosis of these mutations with leukemogenicity in mouse models to better understand the co-dependence of mutations in AML.
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45
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Murakami K, Yamaguchi Y, Kida Y, Morikawa Y, Ujiie H, Sugahara H, Nannya Y, Ogawa S, Kanakura Y. Clonal Cytopenia of Undetermined Significance in a Patient with Congenital Wilms' Tumor 1 and Acquired DNMT3A Gene Mutations. Intern Med 2021; 60:3785-3788. [PMID: 34053991 PMCID: PMC8710374 DOI: 10.2169/internalmedicine.7571-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Congenital mutations of the Wilms' tumor 1 (WT1) gene can lead to various abnormalities, including renal/gonadal developmental disorders and cardiac malformations. Although there have been many reports of somatic WT1 mutations in patients with acute myeloid leukemia and myelodysplastic syndrome, congenital WT1 mutations have not been reported in hematological disorders. We herein report a patient with early-onset clonal cytopenia of undetermined significance that was associated with a congenital mutation of WT1 and an acquired mutation of DNMT3A [encoding DNA (cytosine-5)-methyltransferase 3A].
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Affiliation(s)
- Ken Murakami
- Department of Hematology, Sumitomo Hospital, Japan
| | | | - Yuko Kida
- Department of Hematology, Sumitomo Hospital, Japan
| | | | | | | | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Japan
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46
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Schlosser P, Knaus J, Schmutz M, Dohner K, Plass C, Bullinger L, Claus R, Binder H, Lubbert M, Schumacher M. Netboost: Boosting-Supported Network Analysis Improves High-Dimensional Omics Prediction in Acute Myeloid Leukemia and Huntington's Disease. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2635-2648. [PMID: 32365034 DOI: 10.1109/tcbb.2020.2983010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
State-of-the art selection methods fail to identify weak but cumulative effects of features found in many high-dimensional omics datasets. Nevertheless, these features play an important role in certain diseases. We present Netboost, a three-step dimension reduction technique. First, a boosting-based filter is combined with the topological overlap measure to identify the essential edges of the network. Second, sparse hierarchical clustering is applied on the selected edges to identify modules and finally module information is aggregated by the first principal components. We demonstrate the application of the newly developed Netboost in combination with CoxBoost for survival prediction of DNA methylation and gene expression data from 180 acute myeloid leukemia (AML) patients and show, based on cross-validated prediction error curve estimates, its prediction superiority over variable selection on the full dataset as well as over an alternative clustering approach. The identified signature related to chromatin modifying enzymes was replicated in an independent dataset, the phase II AMLSG 12-09 study. In a second application we combine Netboost with Random Forest classification and improve the disease classification error in RNA-sequencing data of Huntington's disease mice. Netboost is a freely available Bioconductor R package for dimension reduction and hypothesis generation in high-dimensional omics applications.
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47
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Christopher MJ, Katerndahl CDS, LeBlanc HR, Elmendorf TT, Basu V, Gang M, Menssen AJ, Spencer DH, Duncavage EJ, Ketkar S, Wartman LD, Ramakrishnan SM, Miller CA, Ley TJ. Tumor suppressor function of WT1 in acute promyelocytic leukemia. Haematologica 2021; 107:342-346. [PMID: 34670359 PMCID: PMC8719088 DOI: 10.3324/haematol.2021.279601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Indexed: 11/09/2022] Open
Abstract
Not available.
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Affiliation(s)
- Matthew J Christopher
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO.
| | - Casey D S Katerndahl
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - Hayley R LeBlanc
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - Tyler T Elmendorf
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - Vaishali Basu
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - Margery Gang
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - Andrew J Menssen
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - David H Spencer
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO
| | - Shamika Ketkar
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO; Current affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX
| | - Lukas D Wartman
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - Sai Mukund Ramakrishnan
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - Christopher A Miller
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
| | - Timothy J Ley
- Section of Stem Cell Biology, Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO
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48
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Kalushkova A, Nylund P, Párraga AA, Lennartsson A, Jernberg-Wiklund H. One Omics Approach Does Not Rule Them All: The Metabolome and the Epigenome Join Forces in Haematological Malignancies. EPIGENOMES 2021; 5:epigenomes5040022. [PMID: 34968247 PMCID: PMC8715477 DOI: 10.3390/epigenomes5040022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/17/2021] [Accepted: 09/26/2021] [Indexed: 02/01/2023] Open
Abstract
Aberrant DNA methylation, dysregulation of chromatin-modifying enzymes, and microRNAs (miRNAs) play a crucial role in haematological malignancies. These epimutations, with an impact on chromatin accessibility and transcriptional output, are often associated with genomic instability and the emergence of drug resistance, disease progression, and poor survival. In order to exert their functions, epigenetic enzymes utilize cellular metabolites as co-factors and are highly dependent on their availability. By affecting the expression of metabolic enzymes, epigenetic modifiers may aid the generation of metabolite signatures that could be utilized as targets and biomarkers in cancer. This interdependency remains often neglected and poorly represented in studies, despite well-established methods to study the cellular metabolome. This review critically summarizes the current knowledge in the field to provide an integral picture of the interplay between epigenomic alterations and the cellular metabolome in haematological malignancies. Our recent findings defining a distinct metabolic signature upon response to enhancer of zeste homolog 2 (EZH2) inhibition in multiple myeloma (MM) highlight how a shift of preferred metabolic pathways may potentiate novel treatments. The suggested link between the epigenome and the metabolome in haematopoietic tumours holds promise for the use of metabolic signatures as possible biomarkers of response to treatment.
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Affiliation(s)
- Antonia Kalushkova
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (P.N.); (A.A.P.); (H.J.-W.)
- Correspondence:
| | - Patrick Nylund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (P.N.); (A.A.P.); (H.J.-W.)
| | - Alba Atienza Párraga
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (P.N.); (A.A.P.); (H.J.-W.)
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NEO, Karolinska Institutet, 14157 Huddinge, Sweden;
| | - Helena Jernberg-Wiklund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (P.N.); (A.A.P.); (H.J.-W.)
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49
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Maifrede S, Le BV, Nieborowska-Skorska M, Golovine K, Sullivan-Reed K, Dunuwille WMB, Nacson J, Hulse M, Keith K, Madzo J, Caruso LB, Gazze Z, Lian Z, Padella A, Chitrala KN, Bartholdy BA, Matlawska-Wasowska K, Di Marcantonio D, Simonetti G, Greiner G, Sykes SM, Valent P, Paietta EM, Tallman MS, Fernandez HF, Litzow MR, Minden MD, Huang J, Martinelli G, Vassiliou GS, Tempera I, Piwocka K, Johnson N, Challen GA, Skorski T. TET2 and DNMT3A Mutations Exert Divergent Effects on DNA Repair and Sensitivity of Leukemia Cells to PARP Inhibitors. Cancer Res 2021; 81:5089-5101. [PMID: 34215619 PMCID: PMC8487956 DOI: 10.1158/0008-5472.can-20-3761] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/15/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022]
Abstract
Somatic variants in TET2 and DNMT3A are founding mutations in hematological malignancies that affect the epigenetic regulation of DNA methylation. Mutations in both genes often co-occur with activating mutations in genes encoding oncogenic tyrosine kinases such as FLT3ITD, BCR-ABL1, JAK2V617F , and MPLW515L , or with mutations affecting related signaling pathways such as NRASG12D and CALRdel52 . Here, we show that TET2 and DNMT3A mutations exert divergent roles in regulating DNA repair activities in leukemia cells expressing these oncogenes. Malignant TET2-deficient cells displayed downregulation of BRCA1 and LIG4, resulting in reduced activity of BRCA1/2-mediated homologous recombination (HR) and DNA-PK-mediated non-homologous end-joining (D-NHEJ), respectively. TET2-deficient cells relied on PARP1-mediated alternative NHEJ (Alt-NHEJ) for protection from the toxic effects of spontaneous and drug-induced DNA double-strand breaks. Conversely, DNMT3A-deficient cells favored HR/D-NHEJ owing to downregulation of PARP1 and reduction of Alt-NHEJ. Consequently, malignant TET2-deficient cells were sensitive to PARP inhibitor (PARPi) treatment in vitro and in vivo, whereas DNMT3A-deficient cells were resistant. Disruption of TET2 dioxygenase activity or TET2-Wilms' tumor 1 (WT1)-binding ability was responsible for DNA repair defects and sensitivity to PARPi associated with TET2 deficiency. Moreover, mutation or deletion of WT1 mimicked the effect of TET2 mutation on DSB repair activity and sensitivity to PARPi. Collectively, these findings reveal that TET2 and WT1 mutations may serve as biomarkers of synthetic lethality triggered by PARPi, which should be explored therapeutically. SIGNIFICANCE: TET2 and DNMT3A mutations affect distinct DNA repair mechanisms and govern the differential sensitivities of oncogenic tyrosine kinase-positive malignant hematopoietic cells to PARP inhibitors.
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Affiliation(s)
- Silvia Maifrede
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Bac Viet Le
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
- Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Margaret Nieborowska-Skorska
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Konstantin Golovine
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Katherine Sullivan-Reed
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Wangisa M B Dunuwille
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, Missouri
| | - Joseph Nacson
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael Hulse
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Kelsey Keith
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Lisa Beatrice Caruso
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Zachary Gazze
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Zhaorui Lian
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Antonella Padella
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Kumaraswamy N Chitrala
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Ksenia Matlawska-Wasowska
- Division of Hematology-Oncology, Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Daniela Di Marcantonio
- Research Institute of Fox Chase Cancer Center, Immune Cell Development and Host Defense, Philadelphia, Pennsylvania
| | - Giorgia Simonetti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Georg Greiner
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Stephen M Sykes
- Research Institute of Fox Chase Cancer Center, Immune Cell Development and Host Defense, Philadelphia, Pennsylvania
| | - Peter Valent
- Division of Hematology and Hemostaseology and Ludwig-Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Elisabeth M Paietta
- Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, New York
| | - Martin S Tallman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hugo F Fernandez
- Moffitt Malignant Hematology and Cellular Therapy at Memorial Healthcare System, Pembroke Pines, Florida
| | - Mark R Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mark D Minden
- Princess Margaret Cancer Center, Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Jian Huang
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Italo Tempera
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | | | - Neil Johnson
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Grant A Challen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, Missouri.
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine and Sol Sherry Thrombosis Research Center, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania.
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50
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TET3 promotes AML growth and epigenetically regulates glucose metabolism and leukemic stem cell associated pathways. Leukemia 2021; 36:416-425. [PMID: 34462525 DOI: 10.1038/s41375-021-01390-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/07/2021] [Accepted: 08/17/2021] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukemia (AML) is considered a poor prognosis malignancy where patients exhibit altered glucose metabolism and stem cell signatures that contribute to AML growth and maintenance. Here, we report that the epigenetic factor, Ten-Eleven Translocation 3 (TET3) dioxygenase is overexpressed in AML patients and functionally validated human leukemic stem cells (LSCs), is required for leukemic growth by virtue of its regulation of glucose metabolism in AML cells. In human AML cells, TET3 maintains 5-hydroxymethylcytosine (5hmC) epigenetic marks and expression of early myeloid progenitor program, critical glucose metabolism and STAT5A signaling pathway genes, which also positively correlate with TET3 expression in AML patients. Consequently, TET3 depletion impedes hexokinase activity and L-Lactate production in AML cells. Conversely, overexpression of TET3 in healthy human hematopoietic stem progenitors (HSPCs) upregulates the expression of glucose metabolism, STAT5A signaling and AML associated genes, and impairs normal HSPC lineage differentiation in vitro. Finally, TET3 depletion renders AML cells highly sensitive to blockage of the TET3 downstream pathways glycolysis and STAT5 signaling via the combination of 2-Deoxy-D-glucose and STAT5 inhibitor which preferentially targets AML cells but spares healthy CD34+ HSPCs.
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